There isn't any reason why ou can't use any of the single modal window scripts. As you note it would have to be added after the module was published.
It depends what you want to do with it how you implement it.
Remember you'll need to add the script reference somewhere, probably in the start.html header.
The lightwindow code then could be inserted into the 1.xml as a cdata item so that the interpreter js that renders the xml as pages doesn't see it and get freaked.

If it's just to add the effect to a page then an iframe could hold it.